Res: [gmx-users] Topology for nBuOH
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 13 17:10:03 CEST 2011
Juliana Angeiras wrote:
> Hi,
>
> really the problem was with the order, but now i have another problem
> (below). I have already read the chapter 5, but i didn't fix my problem.
> I would like to use an archive .itp for the butanol, although i use the
> tip3p for water in the system (mixture water-butanol), I want
> use different parameters for nonbonded interactions between
> water-butanol (because were parametrized specifically for these
> interactions). How can I do that? My atual archive .top is more below.
>
Again, your directives are out of order. The [nonbond_params] are part of the
top-level force field definition and thus must come before the molecule definitions.
-Justin
> Archive .top:
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 3 yes 0.5 0.5
>
> [ atomtypes ]
> ; name at.num mass charge ptype V(c6) W(c12)
> Hb 1 1.0080 0.38 A 0.4149611E-07 0.9737356E-04
> O 8 15.9994 -0.66 A 0.9722461E-06 0.1247853E-02
> C 6 12.0110 0.40 A 0.4895634E-05 0.2791672E-02
> C 6 12.0110 -0.22 A 0.4895634E-05 0.2791672E-02
> C 6 12.0110 -0.33 A 0.4895634E-05 0.2791672E-02
> H 1 1.0080 -0.06 A 0.4415162E-06 0.5131711E-03
> H 1 1.0080 0.11 A 0.4415162E-06 0.5131711E-03
>
> [ bondtype ]
> ; ai aj funct c0 c1
> Hb O 1 0.10900 462750.4
> O C 1 0.14300 376560.0
> C C 1 0.15300 265265.6
> H C 1 0.10800 284512.0
>
> [ angletype ]
> ; ai aj ak func c0 c1
> C O Hb 1 108.000 460.240
> C C O 1 108.000 418.400
> C C C 1 112.000 488.273
> H C H 1 109.470 292.000
>
> [ moleculetype ]
> ; name nrexcl
> BuOH 3
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 Hb 1 BuOH HO 1 0.38 1.0080
> 2 O 1 BuOH OH 1 -0.66 15.9994
> 3 C 1 BuOH CA 1 0.40 12.0110
> 4 C 1 BuOH CB 1 -0.22 12.0110
> 5 C 1 BuOH CC 1 -0.22 12.0110
> 6 C 1 BuOH CD 1 -0.33 12.0110
> 7 H 1 BuOH HA 1 -0.06 1.0080
> 8 H 1 BuOH Hb 1 -0.06 1.0080
> 9 H 1 BuOH HC 1 0.11 1.0080
> 10 H 1 BuOH HD 1 0.11 1.0080
> 11 H 1 BuOH HE 1 0.11 1.0080
> 12 H 1 BuOH HF 1 0.11 1.0080
> 13 H 1 BuOH HG 1 0.11 1.0080
> 14 H 1 BuOH HF 1 0.11 1.0080
> 15 H 1 BuOH HG 1 0.11 1.0080
>
> [ dihedrals ]
> 1 2 3 4 3 0.41840 1.25520 0.00000 -1.67360 0.00000 0.00000
> 2 3 4 5 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000
> 3 4 5 6 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000
>
> ; Include forcefield parameters
> ;#include "oplsaa.ff/forcefield.itp"
>
> ; Include forcefield parameters
> #include "oplsaa.ff/tip3p.itp"
>
> [ nonbond_params ]
> ; i j func V(c6) W(c12)
> H H 1 0.4149611E-07 0.9737356E-04
> H HW 1 0.4149611E-07 0.9737356E-04
> H C 1 0.4415162E-06 0.5131711E-03
> H O 1 0.1927397E-06 0.3416812E-03
> H OW 1 0.1927397E-06 0.3416812E-03
> H Hb 1 0.4149611E-07 0.9737356E-04
> HW HW 1 0.0000000E+00 0.0000000E+00
> HW C 1 0.4415162E-06 0.5131711E-03
> HW O 1 0.0000000E+00 0.0000000E+00
> HW OW 1 0.0000000E+00 0.0000000E+00
> HW Hb 1 0.4149611E-07 0.9737356E-04
> C C 1 0.4895634E-05 0.2791672E-02
> C O 1 0.2159724E-05 0.1866537E-02
> C OW 1 0.2159724E-05 0.1866537E-02
> C Hb 1 0.4415162E-06 0.5131711E-03
> O O 1 0.9722461E-06 0.1247853E-02
> O OW 1 0.1562282E-05 0.1785000E-02
> O Hb 1 0.0000000E+00 0.0000000E+00
> OW OW 1 0.2510400E-05 0.2552000E-02
> OW Hb 1 0.0000000E+00 0.0000000E+00
> Hb Hb 1 0.4149611E-07 0.9737356E-04
>
> [ system ]
> ; Name
> BuOH in water
>
> [ molecules ]
> ; Compound #mols
> BuOH 343
> SOL 185
>
> Error with grompp:
>
> WARNING 1 [file BuOHaa.top, line 27]:
> Overriding atomtype C
>
> WARNING 2 [file BuOHaa.top, line 28]:
> Overriding atomtype C
>
> WARNING 3 [file BuOHaa.top, line 30]:
> Overriding atomtype H
>
> ERROR 1 [file BuOHaa.top, line 32]:
> Invalid directive bondtype
>
> WARNING 4 [file BuOHaa.top, line 34]:
> Too few parameters on line (source file toppush.c, line 246)
>
> WARNING 5 [file BuOHaa.top, line 35]:
> Too few parameters on line (source file toppush.c, line 246)
>
> WARNING 6 [file BuOHaa.top, line 36]:
> Too few parameters on line (source file toppush.c, line 246)
>
> WARNING 7 [file BuOHaa.top, line 37]:
> Too few parameters on line (source file toppush.c, line 246)
>
> ERROR 2 [file BuOHaa.top, line 39]:
> Invalid directive angletype
>
> WARNING 8 [file BuOHaa.top, line 41]:
> Too few parameters on line (source file toppush.c, line 315)
>
> WARNING 9 [file BuOHaa.top, line 42]:
> Too few parameters on line (source file toppush.c, line 315)
>
> WARNING 10 [file BuOHaa.top, line 43]:
> Too few parameters on line (source file toppush.c, line 315)
>
> WARNING 11 [file BuOHaa.top, line 44]:
> Too few parameters on line (source file toppush.c, line 315)
> Generated 10 of the 10 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 10 of the 10 1-4 parameter combinations
> -------------------------------------------------------
> Program grompp, VERSION 4.5.4
> Source code file: toppush.c, line: 1166
> Fatal error:
> Atomtype opls_111 not found
> Thanks,
>
> Juliana Angeiras B. da Silva.
> Laboratório de Química Teórica e Computacional
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Recife, PE - Brasil.
>
> ------------------------------------------------------------------------
> *De:* Justin A. Lemkul <jalemkul at vt.edu>
> *Para:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Enviadas:* Terça-feira, 12 de Julho de 2011 12:42:49
> *Assunto:* Re: [gmx-users] Topology for nBuOH
>
>
>
> Juliana Angeiras wrote:
> > Hi,
> > I'm trying to include parameters of n-butanol in the topology file
> (below) (i'm not using opls or other force field for butanol), but when
> i run the grompp program, I obtain the following message:
> > Fatal error:
> > Atomtype Hb not found
> > How can I fix this problem?
> >
>
> Your directives are out of order. If you define new atomtypes, etc.
> they have to be defined before they can be used. See Chapter 5 of the
> manual.
>
> -Justin
>
> > Thanks
> > Topology file:
> > ; Include forcefield parameters #include
> "oplsaa.ff/forcefield.itp" ; Include forcefield parameters
> #include "oplsaa.ff/tip5p.itp" [ moleculetype ]
> > ; name nrexcl BuOH 3 [ atoms ] ; nr type resnr
> residu atom cgnr charge mass
> > 1 Hb 1 BuOH HO 1 0.38 1.0080
> > 2 O 1 BuOH OH 1 -0.66 15.9994
> > 3 C 1 BuOH CA 1 0.40 12.0110
> > 4 C 1 BuOH CB 1 -0.22 12.0110
> > 5 C 1 BuOH CC 1 -0.22 12.0110
> > 6 C 1 BuOH CD 1 -0.33 12.0110
> > 7 H 1 BuOH HA 1 -0.06 1.0080
> > 8 H 1 BuOH HB 1 -0.06 1.0080
> > 9 H 1 BuOH HC 1 0.11 1.0080
> > 10 H 1 BuOH HD 1 0.11 1.0080
> > 11 H 1 BuOH HE 1 0.11 1.0080
> > 12 H 1 BuOH HF 1 0.11 1.0080
> > 13 H 1 BuOH HG 1 0.11 1.0080
> > 14 H 1 BuOH HF 1 0.11 1.0080
> > 15 H 1 BuOH HG 1 0.11 1.0080
> > [ atomtypes ]
> > ; name at.num mass charge ptype V(c6) W(c12)
> > Hb 1 1.0080 0.38 A 0.4149611E-07 0.9737356E-04
> > O 8 15.9994 -0.66 A 0.9722461E-06 0.1247853E-02
> > C 6 12.0110 0.40 A 0.4895634E-05 0.2791672E-02
> > C 6 12.0110 -0.22 A 0.4895634E-05 0.2791672E-02 C 6
> 12.0110 -0.33 A 0.4895634E-05 0.2791672E-02
> > H 1 1.0080 -0.06 A 0.4415162E-06 0.5131711E-03
> > H 1 1.0080 0.11 A 0.4415162E-06 0.5131711E-03
> > [ bondtype ] ; ai aj funct c0 c1
> HB O 1 0.10900 462750.4 O C 1 0.14300
> 376560.0 C C 1 0.15300 265265.6 H C 1
> 0.10800 284512.0
> > [ angletype ] ; ai aj ak func c0
> c1 C O HB 1 108.000 460.240 C C O 1
> 108.000 418.400 C C C 1 112.000 488.273
> H C H 1 109.470 292.000
> > [ dihedrals ] 1 2 3 4 3 0.41840 1.25520 0.00000
> -1.67360 0.00000 0.00000
> > 2 3 4 5 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000
> > 3 4 5 6 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000
> > [ nonbond_params ]
> > ; i j func V(c6) W(c12)
> > H H 1 0.4149611E-07 0.9737356E-04
> > H HW 1 0.4149611E-07 0.9737356E-04
> > H C 1 0.4415162E-06 0.5131711E-03
> > H O 1 0.1927397E-06 0.3416812E-03
> > H OW 1 0.1927397E-06 0.3416812E-03
> > H Hb 1 0.4149611E-07 0.9737356E-04
> > HW HW 1 0.0000000E+00 0.0000000E+00
> > HW C 1 0.4415162E-06 0.5131711E-03
> > HW O 1 0.0000000E+00 0.0000000E+00
> > HW OW 1 0.0000000E+00 0.0000000E+00
> > HW Hb 1 0.4149611E-07 0.9737356E-04
> > C C 1 0.4895634E-05 0.2791672E-02
> > C O 1 0.2159724E-05 0.1866537E-02
> > C OW 1 0.2159724E-05 0.1866537E-02
> > C Hb 1 0.4415162E-06 0.5131711E-03
> > O O 1 0.9722461E-06 0.1247853E-02
> > O OW 1 0.1562282E-05 0.1785000E-02
> > O Hb 1 0.0000000E+00 0.0000000E+00
> > OW OW 1 0.2510400E-05 0.2552000E-02
> > OW Hb 1 0.0000000E+00 0.0000000E+00
> > Hb Hb 1 0.4149611E-07 0.9737356E-04
> > [ system ]
> > ; Name
> > BuOH in water
> > [ molecules ]
> > ; Compound #mols
> > BuOH 343
> > SOL 185
> >
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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